Section 2 Claudia Samples

2.1 Experiment

2.2 Metadata

2.3 OligoMM

ID phylum species
YL44 Verrucomicrobia A. muciniphila
I48 Bacteroidetes B. caecimuris
YL27 Bacteroidetes M. intestinale
YL45 Proteobacteria T. muris
YL2 Actinobacteria B. longum
KB1 Firmicutes E. faecalis
KB18 Firmicutes A. muris
YL32 Firmicutes C. clostridioforme
YL31 Firmicutes F. plautii
YL58 Firmicutes B. coccoides
I49 Firmicutes L. reuteri
I46 Firmicutes C. innocuum

2.4 Load in variants

require(data.table)
source("utils.R")
vcftodataframe <- function(vcf_files, contig_mapping = contig_mapping, 
    gff_df = gff_df) {
    require(vcfR)
    res <- list()
    for (file in vcf_files) {
        # message(file)
        vcf_content <- vcfR::read.vcfR(file, 
            verbose = FALSE)
        vcf_fix <- as.data.frame(vcf_content@fix)
        vcf_info <- vcfR::INFO2df(vcf_content)  # contains DP and AF info
        if (nrow(vcf_fix) > 0) {
            # there are variants
            dat <- as.data.frame(cbind(vcf_fix[, 
                c(1, 2, 4, 5, 6)], vcf_info[, 
                c(1, 2)]))
            dat$majorAF <- sapply(dat$AF, 
                minorAfToMajorAf)
            dat$dp <- as.numeric(as.matrix(vcf_info$DP))
            dat$genome <- contig_mapping[match(dat$CHROM, 
                contig_mapping$contig), ]$genome
            dat$genome_hr <- translateGenomeIdToFullName(tolower(dat$genome))
            dat$mouse.id <- substr(tools::file_path_sans_ext(basename(file)), 
                1, 4)
            # add studz type specific annotations
            dat$mouse.group <- designdf[match(dat$mouse.id, 
                designdf$mouse.id), ]$desc
            dat$day <- designdf[match(dat$mouse.id, 
                designdf$mouse.id), ]$day
            dat$generation <- designdf[match(dat$mouse.id, 
                designdf$mouse.id), ]$generation
            dat$ecoli <- designdf[match(dat$mouse.id, 
                designdf$mouse.id), ]$ecoli
            dat$sample <- tools::file_path_sans_ext(basename(file))
            # annotate overlay of gene
            dt_gff <- data.table(start = gff_df$start, 
                end = gff_df$end, chr = as.character(as.matrix(gff_df$chr)), 
                feature = gff_df$product)
            colnames(dat)[1:2] <- c("chr", 
                "start")
            dat$start <- as.integer(as.matrix(dat$start))
            dat$chr <- as.character(as.matrix(dat$chr))
            dat$end <- dat$start
            dat2 <- as.data.table(dat)
            setkey(dt_gff, chr, start, end)
            annotated <- foverlaps(dat2, 
                dt_gff, type = "within", 
                mult = "first")
            res[[tools::file_path_sans_ext(basename(file))]] <- annotated  # add vcf df to list
        } else {
            message("Skipping")
        }
    }
    df <- as.data.frame(do.call(rbind, res))  # merge list to df
    return(df)
}

Merge vcf and annotate with metadata

## data/references/joined_reference_curated_ecoli/joined_reference_curated_ecoli.gff

2.5 Filter out of abnormal high mutation

We filter out samples that have a mutation rate of the global mean.

Mutation profile before removal. Vertical line is the global mean number of mutation rates

Figure 2.1: Mutation profile before removal. Vertical line is the global mean number of mutation rates 

## [1] 22707
Mutation profile after removal. Vertical line is the global mean number of mutation rates befor filtering

Figure 2.2: Mutation profile after removal. Vertical line is the global mean number of mutation rates befor filtering

2.6 AF frequency

## `stat_bin()` using `bins = 30`. Pick
## better value with `binwidth`.

Figure 2.3: AF of resequenced strains 

## `stat_bin()` using `bins = 30`. Pick
## better value with `binwidth`.

Figure 2.4: major AF of resequenced strains

2.7 number of variants per group

2.7.1 number of variants per treatment group

2.7.2 deletion

## geom_path: Each group consists of
## only one observation. Do you need to
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## only one observation. Do you need to
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## geom_path: Each group consists of
## only one observation. Do you need to
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## geom_path: Each group consists of
## only one observation. Do you need to
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## geom_path: Each group consists of
## only one observation. Do you need to
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## geom_path: Each group consists of
## only one observation. Do you need to
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## geom_path: Each group consists of
## only one observation. Do you need to
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## geom_path: Each group consists of
## only one observation. Do you need to
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## geom_path: Each group consists of
## only one observation. Do you need to
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## geom_path: Each group consists of
## only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of
## only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of
## only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of
## only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of
## only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of
## only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of
## only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of
## only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of
## only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of
## only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of
## only one observation. Do you need to
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## geom_path: Each group consists of
## only one observation. Do you need to
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## geom_path: Each group consists of
## only one observation. Do you need to
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## geom_path: Each group consists of
## only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of
## only one observation. Do you need to
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## geom_path: Each group consists of
## only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of
## only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of
## only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of
## only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of
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## geom_path: Each group consists of
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## geom_path: Each group consists of
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## geom_path: Each group consists of
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total number of variants of all 12 OMM genomes by mouse and grouyp stratified by variant type. Seems there is still a outlier (20 cecal content caecimuris, where some samples have more than 1000 varaints)

Figure 2.5: total number of variants of all 12 OMM genomes by mouse and grouyp stratified by variant type. Seems there is still a outlier (20 cecal content caecimuris, where some samples have more than 1000 varaints)

2.8 Heatmap

## Warning in dcast(dat, variant.id ~
## sample, value.var = "AF"): The dcast
## generic in data.table has been passed a
## data.frame and will attempt to redirect
## to the reshape2::dcast; please note
## that reshape2 is deprecated, and this
## redirection is now deprecated as well.
## Please do this redirection yourself
## like reshape2::dcast(dat). In the next
## version, this warning will become an
## error.
## `use_raster` is automatically set
## to TRUE for a matrix with more than
## 2000 rows. You can control
## `use_raster` arugment by explicitly
## setting TRUE/FALSE to it. Set
## `ht_opt$message = FALSE` to turn
## off this message.
AF of all variants (after mutation bias filtering)

Figure 2.6: AF of all variants (after mutation bias filtering)

Variants that are non-zero in every sample (e.g. observed as a variant)

## Warning in dcast(dat, variant.id ~
## sample, value.var = "AF"): The dcast
## generic in data.table has been passed a
## data.frame and will attempt to redirect
## to the reshape2::dcast; please note
## that reshape2 is deprecated, and this
## redirection is now deprecated as well.
## Please do this redirection yourself
## like reshape2::dcast(dat). In the next
## version, this warning will become an
## error.
## [1] 10361

2.9 locations of SNP in genome

## Warning in RColorBrewer::brewer.pal(n, pal): n too large, allowed maximum for palette Dark2 is 8
## Returning the palette you asked for with that many colors
## Warning: Removed 765 rows containing missing
## values (geom_point).

createPositionPlot <- function(chr = "Akkermansia_muciniphila", 
    threshold = 0.3) {
    require("ggrepel")
    library(RColorBrewer)
    
    shapes = group = c(insertion = "+", deletion = "-", 
        SNP = "x")
    dat <- readRDS("data/rds/omm_claudia_new.rds")
    dat <- dat[which(dat$chr == chr), ]
    
    # sum up AF per position to get a measrue
    # of how interesting a location is (e.g.
    # to filter out for which locations we
    # should show a funcitonal annotation)
    
    nb.cols <- 9
    mycolors <- colorRampPalette(brewer.pal(8, 
        "Set2"))(nb.cols)
    
    dat_sum <- aggregate(AF ~ POS + feature + 
        alteration_type, dat, sum)
    dat_sum <- dat_sum[which(dat_sum$AF > 
        threshold), ]
    dat_sum$y <- 1
    numb <- nrow(dat_sum)
    dat_sum$AF <- sample(1:9, numb, replace = TRUE)/10
    if (any(dat_sum$feature == "hypothetical protein")) 
        dat_sum[which(dat_sum$feature == 
            "hypothetical protein"), ]$feature <- ""
    if (any(dat_sum$feature == "outside ORFs")) 
        dat_sum[which(dat_sum$feature == 
            "outside ORFs"), ]$feature <- ""
    
    dat_sum$type <- ifelse(dat_sum$feature == 
        "", "hypo", "annotated")
    
    # get the max AF values per position to
    # get the y coordinate for annotation
    dat_max <- aggregate(AF ~ POS + feature + 
        alteration_type, dat, max)
    dat_sum$AF <- dat_max[match(dat_sum$POS, 
        dat_max$POS), ]$AF
    
    p <- ggplot(dat, aes(x = POS, y = AF, 
        shape = alteration_type, label = feature))
    p <- p + geom_vline(data = dat_sum, aes(xintercept = POS), 
        alpha = 1, color = "grey90")
    p <- p + geom_point(aes(color = mouse.group), 
        size = 2)
    p <- p + scale_color_manual(values = mycolors)
    p <- p + ylim(0, 1)
    p <- p + geom_text_repel(min.segment.length = 0, 
        data = dat_sum, aes(label = feature), 
        size = 2, box.padding = unit(0.35, 
            "lines"), point.padding = unit(0.3, 
            "lines"))
    p <- p + theme_minimal()
    p <- p + scale_shape_manual(values = shapes)
    p <- p + theme(strip.background = element_blank(), 
        strip.text.y = element_text(angle = 0, 
            color = "black"), axis.title.y = element_blank(), 
        axis.ticks.y = element_blank(), axis.line.y = element_blank(), 
        panel.border = element_rect(colour = "black", 
            fill = NA, size = 0.2), panel.grid.major = element_blank(), 
        panel.grid.minor = element_blank())
    p <- p + ggtitle(genome)
    return(p)
}

2.9.1 Akkermansia muciniphila

Position of variants. vertical lines show positions with functional annotation, if no annotation is shown, then its either hypothetical or outside ORF

Figure 2.7: Position of variants. vertical lines show positions with functional annotation, if no annotation is shown, then its either hypothetical or outside ORF 

## Warning in if (nchar(plot$labels$title
## %||% "") > 0) {: the condition has
## length > 1 and only the first element
## will be used
## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

Figure 2.8: Position of variants

2.9.2 B_caecimuris

Position of variants. vertical lines show positions with functional annotation, if no annotation is shown, then its either hypothetical or outside ORF

Figure 2.9: Position of variants. vertical lines show positions with functional annotation, if no annotation is shown, then its either hypothetical or outside ORF 

## Warning in if (nchar(plot$labels$title
## %||% "") > 0) {: the condition has
## length > 1 and only the first element
## will be used
## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

Figure 2.10: Position of variants

2.9.3 Blautia_coccoides

Position of variants. vertical lines show positions with functional annotation, if no annotation is shown, then its either hypothetical or outside ORF

Figure 2.11: Position of variants. vertical lines show positions with functional annotation, if no annotation is shown, then its either hypothetical or outside ORF 

## Warning in if (nchar(plot$labels$title
## %||% "") > 0) {: the condition has
## length > 1 and only the first element
## will be used
## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

Figure 2.12: Position of variants

2.9.4 Clostridioforme

Position of variants. vertical lines show positions with functional annotation, if no annotation is shown, then its either hypothetical or outside ORF

Figure 2.13: Position of variants. vertical lines show positions with functional annotation, if no annotation is shown, then its either hypothetical or outside ORF 

## Warning in if (nchar(plot$labels$title
## %||% "") > 0) {: the condition has
## length > 1 and only the first element
## will be used
## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

Figure 2.14: Position of variants

2.9.5 F_plautii_1

Position of variants. vertical lines show positions with functional annotation, if no annotation is shown, then its either hypothetical or outside ORF

Figure 2.15: Position of variants. vertical lines show positions with functional annotation, if no annotation is shown, then its either hypothetical or outside ORF 

## Warning in if (nchar(plot$labels$title
## %||% "") > 0) {: the condition has
## length > 1 and only the first element
## will be used
## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

Figure 2.16: Position of variants

2.9.6 Muribaculum_intestinale

Position of variants. vertical lines show positions with functional annotation, if no annotation is shown, then its either hypothetical or outside ORF

Figure 2.17: Position of variants. vertical lines show positions with functional annotation, if no annotation is shown, then its either hypothetical or outside ORF 

## Warning in if (nchar(plot$labels$title
## %||% "") > 0) {: the condition has
## length > 1 and only the first element
## will be used
## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

Figure 2.18: Position of variants

2.9.7 T_muris

Position of variants. vertical lines show positions with functional annotation, if no annotation is shown, then its either hypothetical or outside ORF

Figure 2.19: Position of variants. vertical lines show positions with functional annotation, if no annotation is shown, then its either hypothetical or outside ORF 

## Warning in if (nchar(plot$labels$title
## %||% "") > 0) {: the condition has
## length > 1 and only the first element
## will be used
## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

Figure 2.20: Position of variants

2.9.8 Clostridium_innocuum

Position of variants. vertical lines show positions with functional annotation, if no annotation is shown, then its either hypothetical or outside ORF

Figure 2.21: Position of variants. vertical lines show positions with functional annotation, if no annotation is shown, then its either hypothetical or outside ORF 

## Warning in if (nchar(plot$labels$title
## %||% "") > 0) {: the condition has
## length > 1 and only the first element
## will be used
## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

Figure 2.22: Position of variants

2.9.9 Lactobacillus_reuteri_I49_1

Position of variants. vertical lines show positions with functional annotation, if no annotation is shown, then its either hypothetical or outside ORF

Figure 2.23: Position of variants. vertical lines show positions with functional annotation, if no annotation is shown, then its either hypothetical or outside ORF 

## Warning in if (nchar(plot$labels$title
## %||% "") > 0) {: the condition has
## length > 1 and only the first element
## will be used
## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

Figure 2.24: Position of variants

2.9.10 Enterococcus_faecalis.1

Position of variants. vertical lines show positions with functional annotation, if no annotation is shown, then its either hypothetical or outside ORF

Figure 2.25: Position of variants. vertical lines show positions with functional annotation, if no annotation is shown, then its either hypothetical or outside ORF 

## Warning in if (nchar(plot$labels$title
## %||% "") > 0) {: the condition has
## length > 1 and only the first element
## will be used
## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

Figure 2.26: Position of variants

2.9.11 Acutalibacter_muris

Position of variants. vertical lines show positions with functional annotation, if no annotation is shown, then its either hypothetical or outside ORF

Figure 2.27: Position of variants. vertical lines show positions with functional annotation, if no annotation is shown, then its either hypothetical or outside ORF 

## Warning in if (nchar(plot$labels$title
## %||% "") > 0) {: the condition has
## length > 1 and only the first element
## will be used
## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

Figure 2.28: Position of variants

2.9.12 Bifidobacterium_animalis_YL2_1

Position of variants. vertical lines show positions with functional annotation, if no annotation is shown, then its either hypothetical or outside ORF

Figure 2.29: Position of variants. vertical lines show positions with functional annotation, if no annotation is shown, then its either hypothetical or outside ORF 

## Warning in if (nchar(plot$labels$title
## %||% "") > 0) {: the condition has
## length > 1 and only the first element
## will be used
## Warning in geom2trace.default(dots[[1L]][[2L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[2L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

Figure 2.30: Position of variants

2.9.13 Bifidobacterium_animalis_YL2_2

Position of variants. vertical lines show positions with functional annotation, if no annotation is shown, then its either hypothetical or outside ORF

Figure 2.31: Position of variants. vertical lines show positions with functional annotation, if no annotation is shown, then its either hypothetical or outside ORF 

## Warning in if (nchar(plot$labels$title
## %||% "") > 0) {: the condition has
## length > 1 and only the first element
## will be used
## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

Figure 2.32: Position of variants

2.9.14 CP028714.1

Position of variants. vertical lines show positions with functional annotation, if no annotation is shown, then its either hypothetical or outside ORF

Figure 2.33: Position of variants. vertical lines show positions with functional annotation, if no annotation is shown, then its either hypothetical or outside ORF 

## Warning in if (nchar(plot$labels$title
## %||% "") > 0) {: the condition has
## length > 1 and only the first element
## will be used
## Warning in geom2trace.default(dots[[1L]][[2L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning in geom2trace.default(dots[[1L]][[2L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

Figure 2.34: Position of variants